Indoctrination
by RaptorEchelon
Summary: Following Mass Effect 3. Based on the conclusion that Indoctrination Theory is correct. Chapters will be kept to a reasonable length. First is shorter than I'd like, but it had to end where it did. Female Shepard, Paragon Infiltrator.


**Indoctrination**

In raising her side arm, Commander Mara Shepard knew this was the end. The Intelligence-The Catalyst- had made it very clear she would not only destroy the Reapers, but every Synthetic in the Galaxy. The Relays too would be destroyed. The relays could be rebuilt but a part of her still wasn't sure if she could consign the Geth and EDI to die. Joker would be heartbroken, and the Quarians were more reliant on their new allies than they would like to admit. Still she knew this was the only way to see Liara again, to have children and live a normal life. Was that selfish of her? Probably.

So she fired, and again. The large Paladin handgun almost too much for her weak arms to take at this point. She ignored the rattling in her wrists and fired again and again. The machinery in front of her exploding. When the weapon would fire no more, she dropped the weapon and collapsed.

Lying on her back she saw through the window that a red light was beginning to emanate from the Crucible. It began to spread, and when it came into contact with a Reaper it would explode. Then, as the the last friendly ship left made the jump out of the system, the Crucible fired, a red beam of energy that struck out into space. She knew it had hit the Charon Relay at Pluto, and that form there it would spread, destroying the Reapers and all Synthetic life. For a second, she felt an overwhelming sense of guilt, how was this any better than the Reapers? She had doomed an entire race to die. A race that, thanks to her, was now fully sentient. Each Geth Platform now a fully actualised personality. Then there was EDI. The Normandy's AI, and her new body, flashed through Commander Shepard's mind. Then the Crucible exploded, and even though she would likely never see Liara again, Mar Shepard smiled.

_Reaper "indoctrination" is an insidious means of corrupting organic minds, "reprogramming" the brain through physical and psychological conditioning using electromagnetic fields, infrasonic and ultrasonic noise, and other subliminal methods _

_-Codex__ Entry on Indoctrination_

She could breathe. At first she imagined she was in Heaven, and that she was breathing there. Except when she took a breath the air was acrid, hot, and the smell of death had found its way into her nostrils. Then sound came, the sound of a distant battlefield, and dim muffled voices. A part of her knew she could open her eyes but what would she see?The though terrified her, after all...she was dead.

At first it hurt too much to open them, but when she finally did she was confused. This was Earth, London. In fact she was right next to the Conduit beam. She was so confused by that fact that she didn't notice the Reapers standing over her. Four massive ships, surrounding her. She knew the one in front of her was Harbinger. She tried to get off her back and run but she couldn't. Her body hut too much and in too many places. The attempt to stand caused her to scream.

Then she saw, the Reapers were dead, not lights on their eyes, they had slumped to one side, disabled. Had she done it then? Why hadn't they exploded?

"She's alive! Someone get a medic up here!" The voice was distant, but she managed to turn her head and saw marines. The Alliance symbol on their chests bright against the dim light. Before she could process anymore they were picking her up and putting her on a stretcher. How had she got here? The Crucible had exploded.

Familiar faces appear over her briefly. Garrus, Wrex, Tali. Then Liara,who was crying, yet smiling at the same time. Then they were gone, and she was being loaded onto a shuttle. Which took off, and left her more confused than ever.

_Slow, patient indoctrination allows the thrall to last for months or years. _

Lieutenant Marcus Wright was an N7 class Marine. That meant he had seen action throughout Systems Alliance space. Nothing could have prepared him for Earth however. The final run to the beam had been desperate, a last chance to save the Galaxy. Then it failed. Harbinger had landed and brought destruction to the Hammer forces. Marcus had dived behind a blown out Mako for cover, and waited for death. When it never came he look out onto the field and saw Commander Shepard. She was the only person there, the only one still alive. Four Reapers had surrounded her but they weren't moving. It was as though Harbinger had locked himself into a staring contest with this solitary figure. For maybe ten minutes the Reapers and Shepard had stood there. Marines were coming out of cover, and regrouping. Orders were given to mass on the beam and save the Commander. Then the Reapers slumped over, and the Commander collapsed.

Everything moved faster after that, Marcus was running for the beam whilst Medics got the Commander to safety. Soon a Krogan was joining him, and a Turian, as well as some other Marines. They had all hit the beam whilst the Reapers guarding it seemed disabled. The ones in space weren't, the Crucible needed to be activated.

The Beam brought them out at the bottom steps of the Presidium, and bringing his M8 rifle to bear Marcus began to move. Reaper Husks blocked the stairs but they fell to concentrated rifle fire. Skirting around the room the squad hit the next set of stairs. Marcus and two marines took the ones on the left and everyone else went right. The Krogan was busy with Ravager units, and the Turian had Husks all over him. Still Marcus moved. As they made it to the final steps he realised he had never been to this part of the Citadel. The council had made Shepard a Spectre here. He had watched the vids. So he knew this was also where Saren Arterius was finally beaten.

As another Marine fell to gunfire, Marcus made it to the top. Ahead of him was a large console, and behind that the podium the Council had often stood on. These thoughts distracted him long enough for a Marauder to hit him, the round piercing his chest. As Medi-Gel began to pour over the wound and his suit auto locked on the impact sit, he turned and fired. The Marauder collapsed down the stairs.

The console now in front of him, Marcus saw only one major command:

**FIRE CRUCIBLE**

Who knew what ancient race had created the programming to detect the super weapon, but he thanked them for making it simple now. Slamming his fist onto the command button another round pierced his shoulder. Falling backwards Marcus saw the Crucible light up from where it met the Presidium and fire. The Marauder approaching to finish him was dissolved into atoms before it could kill him, but he wouldn't have needed to anyway.

Lieutenant Marcus Wright's last thought was of Earth, and of home.

_Should a Reaper subvert a well-placed political or military leader, the resulting chaos can bring down nations. _

The world was white. Bright fluorescent lights hurt her eyes and dim voices hurt her head. As the world came into focus, Mara saw the white was that of a hospital roof. The voices were fo someone at the feet of her bed. Struggling to sit up, Shepard felt a hand on her shoulder, and looked to her left. The owner of that hand was someone she thought had died.

"EDI?"


End file.
